Genotyping Assays on the Illumina BeadStation
Infinium genotyping
Infinium Genotyping BeadChips are based on Illumina's BeadArray technology, which provides 100% quality control and high feature redundancy. The Infinium Assay allows large-scale interrogation of variations in the human genome, accelerating the ability of researchers to cost-effectively unlock the genetic basis of disease. Infinium products include genome-wide solutions and iSelect Infinium Custom Genotyping Panels. The Infinium Assay protocols feature single-tube sample preparation without PCR or ligation steps reducing potential sample handling errors. An enzymatic discrimination step provides high call rates and accuracy with unconstrained locus selection.
The Infinium products are shown below:
Infinium BeadChips |
SNPs/Markers | |
|---|---|---|
>240,000 |
|
|
>510,000 |
genotypes 2 samples simultaneously |
|
>683,000 |
|
|
>620,000 |
genotypes 4 samples simultaneously |
|
>1,000,000 |
genotypes 2 samples simultaneously |
|
>370,000 |
genotypes 4 samples simultaneously |
|
6,090 |
genotypes 12 samples simultaneously |
|
7,600-60,800 |
genotypes 12 samples simultaneously |
Click here for a more detailed explanation of the Infinium genotyping assay.
GoldenGate SNP Genotyping
Custom SNP panels - GoldenGate Custom Panels provide flexibility and high data quality across a wide range of genomes and experimental designs. GoldenGate Custom Panels are available in panels of 96 and 384 - 1,536 assays per OPA tube. Genizon's expert team of bioinformaticians will work with you and Illumina's technical support team to optimize the selection of your custom SNP set. The typical conversion rate from selected SNPs to high quality assays, following extensive in-silico prescreening of the loci, is approximately 90%.
Genizon can apply any of Illumina's focused content SNP panels:
- Human Linkage Panel V - 6,056 SNPs uniformly distributed across the genome, optimized for linkage mapping studies.
- Mouse Low Density Linkage Panel - 377 SNPs optimized for application to N2 and F2 mouse genetics crosses that can be used for mapping quantitative trait loci.
- Mouse Medium Density Linkage Panel - 1,449 SNPs optimized for various mapping applications including characterization of transgenic, congenic, and knockout animals, and genetic mapping in advanced intercross mouse lines.
- Major Histocompatibility Complex (MHC) Panel set - Consists of two oligonucleotide assay pools, the MHC Mapping Panel and the MHC Exon-Centric Panel. These two panels can be used independently or combined for more comprehensive coverage. Each panel offers a cost-effective and flexible method for mapping disease-associated variants in the MHC region. This 2,360-loci set has an average 2 kb between each SNP.
- MHC Exon-centric panel - 1,228 SNPs within 10 kb of coding sequences in the MHC.
- MHC Mapping panel - 1,293 SNPs across the MHC at an average spacing of 3.8 kb.
- Cancer SNP Panel - 1,421 SNPs chosen from the National Cancer Institute's (NCI) Cancer Genome Anatomy Project SNP500 Cancer Database. The Cancer SNP Panel can be deployed on the 96-sample Sentrix® Universal Array Matrix and the 16-sample Sentrix Universal BeadChip.
- African American admixture panel - 1,509 SNPs optimized for admixture mapping studies in African American populations.
- HumanCVD BeadChip contains more than 49,000 SNP probes targeting ~2,100 candidate genes associated with cardiovascular disease (CVD) and other associated phenotypes
- DNA test panel consists of 360 thoroughly screened and validated SNP loci, for pre-screening DNA samples for assay performance before conducting studies with larger numbers of loci.
- BovineSNP50 BeadChip more than 54,000 evenly spaced probes
- CanineSNP20 BeadChip contains 22,362 evenly spaced, highly informative SNP probes
- EquineSNP50 BeadChip more than 54,000 highly informative SNPs